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Our Team

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Dr. Yogesh Shouche

Research experience of 28 years in the field of microbial ecology, microbial molecular taxonomy and biodiversity.More than 330 publications in reputed journals of relevant area.Reviewed publications in International journals like FEMS Ecology, International Journal of Systematic and Evolutionary Microbiology, Microbial Ecology and others.

Several national and international collaborations; more than 25 successful grant applications from various funding agencies. Seventeen students awarded PhD from University of Pune and Eight are currently registered.Twenty years of post-graduate teaching experience and five years teaching experience for M.Sc. students.

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Dr. Dhiraj Dhotre

Dr. Dhiraj’s interest lies in the field of Microbial genomics and metagenomics. He is an expert in Bioinformatics and is involved in developing and standardizing the data analysis pipelines at ‘The YSS Lab’. His main research interest lies in the field of human microbiome in health and disease, and has been extensively working in this field for more than 10 years. He is also actively involved in the projects for taxonomic characterization of microbial isolates. He completed his Ph.D. in Biotechnology at the National Centre for Cell Science and had worked on Generation, annotation, and analysis of ESTs from midgut tissue of adult female Anopheles stephensi mosquitoes. Along with these areas, his current research work is also focused on biomethanation potential of landfill methanogens and Development of Efficient and Low Cost Biotechnology for Colour Removal of Spent wash from Distillery.

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Dr. Omprakash Sharma

I completed my M. Sc. and Ph.D. in Microbiology from Dr. RMLU, Faizabad and ‘University of Delhi’ respectively in the area of bacterial taxonomy and bioremediation of pollutants contaminated sites. Received 4.5 years postdoctoral training from Florida State University, FL, USA and Georgia Institute of Technology, Atlanta, USA in the area of anaerobic microbiology and bioremediation of uranium and nitrate contaminated subsurface groundwater.

During my journey of research, I have developed expertise in anaerobic microbiology, bacterial culturomics and taxonomy, bacterial physiology and metabolism, human gut-metaproteomics using next generation LC-MS/MS and Bottom-up proteomics approach and global meta-metabolomics. I try to employ above expertise in my projects to seek the solution of problems related to Taxonomy, Energy, Environment, and Microbial Ecology. Cultivation of tough to cultivate strict anerobic Bacteria and Archaea from anaerobic habitats (human gut, wastewater treatment plant, landfill leachate) using high throughput culturomics approaches and their taxonomical characterization and inventory preparation is one of the aspects of my ongoing research. In addition, along with Dr. Shouche, I am also trying to understand what type of microbiota is physiologicaly active and dominating in obese vs malnourshied individual using Bottom up-Metaproteomics approach.

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Dr. Shrikant Pawar

Dr. Shrikant's research interest lies in the field of Astrobiology, bacteria associated with Marine sponges, and also in high throughput bacterial culturomics and screening for various industrially important enzymes. He is the CO-PI to Marine component of the “Maharashtra Gene Bank Programme” funded by RGSTC, Maharashtra. The 5 year project deals with the molecular barcoding of Marine Sponges and assessment of microbial diversity associated with them by using next generation sequencing. His interest also lies in screening for ice nucleating bacteria and bacterial isolates for significant probiotic properties both on phenotypic and genotypic level. He is involved in a few microbial genomics projects and carry out studies to elucidate their functional role in various environmental niches e.g. Probiotics, ice nucleating bacteria and restoration of environmental sites (Methanotrophs) etc. He is actively involved in various outreach activities and is the Joint secretary of the Association of Microbiologists of India (Pune Chapter).

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Dr. Praveen Rahi

My research interests are evolutionary relationship among the legume-rhizobia (particularly crop legumes), rhizosphere microbiome and microbial taxonomy. I have deciphered a biogeographic pattern of distribution of two different sublineages of pea rhizobia in the two valleys of the Indian trans-Himalayas. Recently, I surveyed the different agro-climatic regions of Indian to study the population structure of pea rhizobia and found that specific species of Rhizobium nodulates pea in different regions. I am also undertaking the comparative genome and pan-genome analyses of different species of pea-Rhizobium. To get a better understanding of microsymbiont selection by legumes, I am exploring the bacterial communities in the rhizosphere using NGS technologies. The overall scientific goal of my research is to harness microbiome of plants to increase farm productivity via increasing nutrient uptake and cycling, and resistance of disease incidence.

I am also interested in the detection of “objectionable microorganisms”, which can either cause illness or degrade the products. Identifying them up to species and sub-species levels, and to know which places they prefer to proliferate could provide crucial information to develop highly efficient strategies to control microbial infections and contaminations.

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Dr. Avinash Sharma

My research is focused on the analysis of bacteria and archaeal communities from different environmental niches (extreme and aquatic environments) using culture independent approaches in microbial genomics to understand how they function under different environmental scenario. The other primary research objective of my study is to cultivate yet to culture microbes to exploit them for novel secondary metabolites and their identification using modern taxonomic approaches in microbiology.

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Dr. Dhiraj Paul

He is working as a DST Young Scientist. Currently, Dhiraj is working on geomicrobiology of Lonar Lake ecosystem. It is a hypersaline and hyperalkaline Soda Lake and an extraterrestrial impact crater formed on volcanic-flood basaltic rocks. Therefore, it is an excellent site for astrobiologist to study analogous life present on basaltic impact crater structures that are present on the surfaces of Mars and the Moon. He is involved in understanding how the environmental conditions of Lonar Lake shape the indigenous microbial community structure and their function.

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Dr. Kumar Siddharth Singh

Siddharth is an observer by nature and a biotechnologist by choice. He has received training in protein science to study host-microbe interactions during his PhD (Animal Biotechnology) and in pharmaceutical biotechnology during his MSc. (Biotechnology). Currently, working as DST-SERB National Postdoctoral Fellow, he is working on a project to determine the status of antimicrobial resistance in sewage. His prime focus is to unravel antimicrobial resistance as a complex interplay of host-microbe-host cross talk. He has interests in sewage metagenomics, gene cloning and expression, study of ligand-receptor interactions.

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Dr. Snehal Kulkarni

Snehal is working as an early career scientist under DBT-BIOCARE Scheme. She completed her doctoral work from MACS-Agharkar Research Institute, Pune on production of biodegradable polymer by extremophilic bacteria isolated from Lonar Lake, India. She is particularly interested in production and characterization of exopolysaccharides (EPS) of halophilic archaea isolated from saline ecosystems of West Coast of India. The main aim of her study is to isolate halophilic archaea from different saline ecosystems located near West Coast of India particularly in Western Maharashtra and explore them for production of EPS.

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Dr. Kusum Dhakar

Kusum is a Post-doctoral fellow working at the YSS lab, National Centre for Microbial Resource, Pune. She is interested in the diversity and bioprospection of cold adapted microorganisms. Her Ph.D. work was focused on lignin degrading potential of psychrotolerants (bacteria & fungi) along with the diversity. At present her research work is related to the microbial community structure and its involvement in the ecological processes associated to the Indian Himalaya.

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Dr. Preeti Neema

Origin of life on Earth and Microbiology of extreme and specialized environments intrigue me. As a Post-doctoral Researcher, currently Preeti is investigating microbial diversity in varied niches ranging from Himalayan hot springs to deep subsurface sediments from mineral rich Indian continental margin. Her interest in Astrobiology has led her to become a part of an International Astrobiology Expedition at Ladakh, India (2016). Apart from research, she is also actively involved in science communication and outreach program through delivering talks on radio and in rural schools. When not doing science, she likes to paint, travel and play with her three YO daughter.

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Shreyas Kumbhare

A science enthusiast and a senior research fellow, Shreyas is interested in understanding the factors influencing the gut microbiome of children, especially the host factors such as FUT2 secretor status and birth mode. His work is also focused upon exploring and tracking the changes in the gut microbiome during pregnancy and its association with the gut microbial diversity of infants in the early stages. Although a microbiologist by training, he is also working on various projects using computational approaches in genomics, metagenomics and phyogenetics.

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Diptaraj Chaudhari

Diptaraj is currently working as a senior research fellow and pursuing a Ph.D. in human microbiome and bioinformatics in the YSS Lab, where he is studying the age related changes in the bacterial microbiome of human gut, skin and oral ecosystems of the patrilineal joint families. Prior to joining for Ph.D., Diptaraj obtained his M.Sc. in biotechnology from North Maharashtra University where he studied the protease inhibitors from Lawsonia inermis.

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Kunal Jani

He is a graduate student with a research focus in the field of Environmental Microbiology, Molecular Ecology and Microbial Systematics. He is currently involved in a project which aims to assess the alterations in the microbial diversity during the world’s largest mass gathering event (MGE), the Kumbh-Mela and to elucidate its impact on the river ecosystem and human health. He has a special interest towards extremophiles that thrives at diverse ecological niches viz. Soldhar Hot Springs, Deep sea sediments and Glacier sediments from Arctic.

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Vikas Ghattargi

A graduate in biotechnology engineering, Vikas has previously worked with human genetics and has now diverted his research interests in probiotics, as he quotes “It's all about gut. Editing - it's always about gut”. Currently, he is exploring the Human Gut Microbiota for their hidden probiotic potential by culturomics. His work involves isolation, functional and genome characterization for indigenous gut isolates thus gain insights into functions ascribed with them. He is also involved in genomics of commonly used probiotic genera and little steps toward translation research.

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Akshay Gaike

Akshay, a trekking enthusiast and a graduate student, works on investigating the potential role of microbiome in disease and its impact on host health. Currently, he is tracking the shift of microbiota in diabetic individuals, undergoing antidiabetic treatment and newly diagnosed diabetic individuals in comparison with healthy individuals. He is also trying to associate his findings with various biochemical parameters and immunological aspect using metagenomics as well as metatranscriptomics approach. He is also actively involved in different projects ranging from characterization of lung microbiome in healthy and COPD disease cohort exposed to biomass as well as tobacco smoking and comparative genomics of pathogens.

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Deepak Khairnar

Deepak is strong believer of the quote: “Science is more about observations! Observations that we get through our daily experiences, so be an adventurous, traveler and explore this beautiful earth”. He is postgraduate student in biotechnology and pursuing his PhD degree from NCCS Pune, under the guidance of Dr. Shouche. He has been always curious about the role of microbes in nature especially their associations with other organisms. This curiosity has led him to do his PhD degree on host-microbe interactions and understanding the immense role of microbes on the planet Earth.

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Sahabram Dewala

Sahabram is currently working on isolation and characterization of human gut microbiota involved in gluten metabolism and also finds the specific bacterial gene responsible for detoxification of immunogenic gluten and its corresponding pathway through whole genome analysis. His study involves cloning the gluten metabolizing bacterial gene and examining its expression. This study may find new gluten metabolizing bacteria that could consider as good source of probiotic in Celiac Disease.

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Satish Yadav

Satish is a Ph.D. scholar at the YSS lab and is interested in exploring the microbiology of Lonar Lake and its inflow ‘Dhara”. He is looking at profound culturable and uncultured microbial diversity of Lonar lake. Using shotgun metagenomics, he is exploring various genes involved in biogeochemical and nutrient cycles operational in highly alkaline pH. Use of meta-metabolomics and CLPP to unveil novel biological pathways which are likely to be unique to halo-alkaline ecosystems is also a part of his study.

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Rahul Bodkhe

Rahul, at present is involved in a study which aims to understand the role of the gut microbiota in gastrointestinal diseases which are affecting the majority of the population worldwide and are one of the reasons for malnutrition in children. In future, he wishes to work for the better health of children affected by malnutrition and gastrointestinal diseases. He believes his present research problem will lead him to help resolve the problem of child intestinal diseases and malnutrition, through microbiome research.

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Abhijit Kulkarni

A music aficionado by heart, Abhijit has obtained his Master’s in Microbiology from the University of Pune. Currently a Graduate student, he is engaged in understanding the tribal microbiome of the Rongmei community from North-East India. He also plans to use extensive culturomics to probe microbes indigenous to the Indian population. When free, he can be found volunteering for classical arts appreciation amongst school children and works passionately to spread the joy of Microbial Science to the public.

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Rakeshkumar Yadav

He believes in “performing a research for Humanity. Let’s keep a goal of serving the humanity.” Rakeshkumar completed his Masters in Microbiology from The Maharaja Sayajirao University of Baroda (2016). He is working currently in the project entitled as “The Maharashtra Gene Bank Programme” under the able guidance of Dr. Yogesh Shouche, NCCS, Pune. Basically, the project deals with the molecular barcoding of Marine Sponges and its microbial diversity assessments by using next generation sequencing and its analysis. He is also involved in a project which involves stratospheric sampling of microbes and their isotopic ratio analysis by using NanoSIMS.

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Abhishek Keer

He did his bachelors in Biochemistry from Barakatullah University and masters from DAVV Indore. Currently he is working on Anti-Microbial Resistance (AMR) and his research interests include metagenomics approaches in microbial ecology and human health. Besides being a researcher he is a fitness freak and love cycling and spending time in gym.

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Dattatray Mongad

“Only free and open mind can seek a way out of maze” he believes in being that maze runner, who tries to seek relevant information in Biological Data (I will like to call it DataMaze). Dattatray is a PhD student in the YSS Lab at National Centre for Cell Science. He has completed his master’s degree in Bioinformatics and interested in predictive, computational and systems biology. Currently, his focus is on understanding the ‘Effect of dysbiosis in human health and disease’.

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Kamala Sape

Kamala is a PhD student and has recently joined the lab and is working under the guidance of Dr. Yogesh Shouche. I did my masters in Microbiology from Andhra University, Visakhapatnam. “Being a Microbiologist, I do believe when there is a question unanswered that how the things are actually happening around us, there would be the existence of microbe to resolve the whole thing”. In the YSS lab team she has started exploring the innovative self & microbiome as well.

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Sayali Dongre

The way how nature works has always fascinated me. Learning about the complexity of life and organisms not even visible to the naked eye made me eager to work and understand more about the subject. I have graduated as MSc. Biotechnology, currently working in NCMR as a Junior Research Fellow. My work involves isolation of new microbes and screening of available cultures for color removal of distillery spent wash. Release of untreated spent wash in rivers pollutes water resulting in hazardous impact on aquatic life. Promising cultures efficient in decolorizing spent wash and reducing its toxicity will be selected after qualitative and quantitative analysis, in order to achieve our aim of developing low cost biotechnology for the treatment of spent wash.

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Shalaka Patil

Learning about diverse niches of microorganisms boosted my fascination to espy more about these living entities. I have pursued Masters of Science with Microbiology as the principle subject. My keen desire is to unearth life dwelling in extreme environments like at high or low temperatures, in anaerobic conditions like landfills, deep seafloors, extreme acidic or alkaline environments, etc. At present, my work is to inspect the microbial diversity functional within the landfills, primarily, my research involves study of biochemical nature of landfill samples of different regions, designing a medium which shall harbour the natural microbiome specifically methanogens. Methanogens survive in anoxic conditions and have significant role in methane gas production. Further, application shall include generation of bioenergy using different feedstocks via anaerobic digestion.

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Anusha Priya

“How life originated” is a question that has intrigued me always, which is why I chose life sciences as my line of work. The ever changing, ever evolving plethora of life, which incessantly adapts to those changes, is what inspires me to work in this field. A master’s graduate, I recently started working at NCMR as a Junior Research Fellow. My current work involves screening of bacterial and fungal cultures for color removal from distillery effluent (a.k.a. spent wash). Spent wash is rich in dark brown pigments called Melanoidins which are recalcitrant in nature. My work is mainly focused on selecting a microbial culture that can effectively decolorize spent wash and thus develop a low cost biotechnology that can lower BOD and COD values while achieving successful decolorization.

Dr. Shrikant Bhute Dr. Mangesh Suryawanshi Dr. Sunil Banskar Pranav Pande
Kunal Yadav Mohit Navandar Sushant Parab Dr. Kiran Mahale
Sudarshan Shetty Somak Chowdhury Dr. Nachiket Marathe Dr. Snehit Mhatre
Dr. Himanshu Kumar Dr. Girish Kulkarni Dr. Prashant Pandey Dr. Rahul Salunkhe
Dr. Sandeep Walujkar Dr. A.K.Gupta Dr. C.P.Anthony Dr. Swapnil Gaikwad
Dr. Mahesh Dharne Dr. Kamlesh Jangid Dr. Amit Yadav